Identifying complex motifs in massive omics data with a variable-convolutional layer in deep neural network.

Motif identification is among the most common and essential computational tasks for bioinformatics and genomics. Here we proposed a novel convolutional layer for deep neural network, named variable convolutional (vConv) layer, for effective motif identification in high-throughput omics data by learning kernel length from data adaptively. Empirical evaluations on DNA-protein binding and DNase footprinting cases well demonstrated that vConv-based networks have superior performance to their convolutional counterparts regardless of model complexity. Meanwhile, vConv could be readily integrated into multi-layer neural networks as an 'in-place replacement' of canonical convolutional layer. All source codes are freely available on GitHub for academic usage.

Expectation pooling: an effective and interpretable pooling method for predicting DNA-protein binding.

MOTIVATION: Convolutional neural networks (CNNs) have outperformed conventional methods in modeling the sequence specificity of DNA-protein binding. While previous studies have built a connection between CNNs and probabilistic models, simple models of CNNs cannot achieve sufficient accuracy on this problem. Recently, some methods of neural networks have increased performance using complex neural networks whose results cannot be directly interpreted. However, it is difficult to combine probabilistic models and CNNs effectively to improve DNA-protein binding predictions. RESULTS: In this article, we present a novel global pooling method: expectation pooling for predicting DNA-protein binding. Our pooling method stems naturally from the expectation maximization algorithm, and its benefits can be interpreted both statistically and via deep learning theory. Through experiments, we demonstrate that our pooling method improves the prediction performance DNA-protein binding. Our interpretable pooling method combines probabilistic ideas with global pooling by taking the expectations of inputs without increasing the number of parameters. We also analyze the hyperparameters in our method and propose optional structures to help fit different datasets. We explore how to effectively utilize these novel pooling methods and show that combining statistical methods with deep learning is highly beneficial, which is promising and meaningful for future studies in this field. AVAILABILITY AND IMPLEMENTATION: All code is public in https://github.com/gao-lab/ePooling. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Causal effects of informal care and health on falls and other accidents among the elderly population in China.

PURPOSE: This article analyzes the causal effects of informal care, mental health, and physical health on falls and other accidents (e.g., traffic accidents) among elderly people. We also examine if there are heterogeneous impacts on elderly of different gender, urban status, and past accident history. METHODS: To purge potential reversal causal effects, e.g., past accidents induce more future informal care, we use two-stage least squares to identify the impacts. We use longitudinal data from a representative national China Health and Retirement Longitudinal Study of people aged 45 and older in China. A total of 3935 respondents with two-wave data are included in our study. Each respondent is interviewed to measure health status and report their accident history. Mental health is assessed using CES-D questions. RESULTS: Our findings indicate that while informal care decreased the occurrence of accidents, poor health conditions increase the occurrence of accidents. We also find heterogeneous impacts on the occurrence of accidents, varying by gender, urban status, and past accident history. CONCLUSIONS: Our findings suggest the following three policy implications. First, policy makers who aim to decrease accidents should take informal care of elders into account. Second, ease of birth policy and postponed retirement policy are urgently needed to meet the demands of informal care. Third, medical policies should attach great importance not only to physical health but also mental health of elderly parents especially for older people with accident history.

Spatial-linked alignment tool (SLAT) for aligning heterogenous slices.

Spatially resolved omics technologies reveal the spatial organization of cells in various biological systems. Here we propose SLAT (Spatially-Linked Alignment Tool), a graph-based algorithm for efficient and effective alignment of spatial slices. Adopting a graph adversarial matching strategy, SLAT is the first algorithm capable of aligning heterogenous spatial data across distinct technologies and modalities. Systematic benchmarks demonstrate SLAT's superior precision, robustness, and speed over existing state-of-the-arts. Applications to multiple real-world datasets further show SLAT's utility in enhancing cell-typing resolution, integrating multiple modalities for regulatory inference, and mapping fine-scale spatial-temporal changes during development. The full SLAT package is available at https://github.com/gao-lab/SLAT .

Simian genogroup I picobirnaviruses: prevalence, genetic diversity, and zoonotic potential.

We previously reported the first detection of simian picobirnaviruses (PBVs) by polyacrylamide gel electrophoresis in fecal specimens of two monkeys with diarrhea in China. We now report the detection of genogroup I PBVs in 48% (44/92) of the fecal specimens by reverse transcriptase PCR (RT-PCR) and amplicon sequencing using primers specific for the RNA-dependent RNA polymerase (RDRP) gene. Molecular characterization of these 44 strains demonstrated both sequence conservation and diversity among simian PBVs and among simian, porcine, and human PBVs. We further determined full-length sequences of segment 2 of the two simian PBV strains, monkey/CHN-14/2002 and monkey/CHN-49/2002, and demonstrated 52.5% to 54.2% nucleotide sequence similarity to the corresponding gene of the bovine strain RUBV and the prototype human strain 1-CHN-97 of genogroup I PBVs and an even lower similarity (38.4%) to segment 2 of the prototype human genogroup II strain 4-GA-91. Further studies are needed to investigate the epidemiology and pathogenesis of PBVs in animals and humans.

Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis.

Alcoholic hepatitis is a major health care burden in the United States due to significant morbidity and mortality. Early identification of patients with alcoholic hepatitis at greatest risk of death is extremely important for proper treatments and interventions to be instituted. In this study, we used gradient boosting, random forest, support vector machine and logistic regression analysis of laboratory parameters, fecal bacterial microbiota, fecal mycobiota, fecal virome, serum metabolome and serum lipidome to predict mortality in patients with alcoholic hepatitis. Gradient boosting achieved the highest AUC of 0.87 for both 30-day mortality prediction using the bacteria and metabolic pathways dataset and 90-day mortality prediction using the fungi dataset, which showed better performance than the currently used model for end-stage liver disease (MELD) score.

Moderate Alcohol Use Is Associated with Reduced Cardiovascular Risk in Middle-Aged Men Independent of Health, Behavior, Psychosocial, and Earlier Life Factors.

We examined whether the often-reported protective association of alcohol with cardiovascular disease (CVD) risk could arise from confounding. Our sample comprised 908 men (56−67 years), free of prevalent CVD. Participants were categorized into 6 groups: never drinkers, former drinkers, and very light (1−4 drinks in past 14 days), light (5−14 drinks), moderate (15−28 drinks), and at-risk (>28 drinks) drinkers. Generalized linear mixed effect models examined the associations of alcohol use with three established CVD risk scores: The Framingham Risk Score (FRS); the atherosclerotic CVD (ASCVD) risk score; and the Metabolic Syndrome (MetS) Severity score, adjusting for group differences in demographics, body size, and health-related behaviors. In separate models we additionally adjusted for several groups of potentially explanatory factors including socioeconomic status, social support, physical and mental health status, childhood factors, and prior history of alcohol misuse. Results showed lower CVD risk among light and moderate alcohol drinkers, relative to very light drinkers, for all CVD risk scores, independent of demographics, body size, and health-related behaviors. Alcohol-CVD risk associations were robust to further adjustment for several groups of potential explanatory factors. Study limitations include the all-male sample with limited racial and ethnic diversity, and the inability to adjust for sugar consumption and for patterns of alcohol consumption. Although this observational study does not address causation, results show that middle-aged men who consume alcohol in moderation have lower CVD risk and better cardiometabolic health than men who consume little or no alcohol, independent of a variety of health, behavioral, psychosocial, and earlier life factors.

[Construction of lentiviral mediated CyPA siRNA and its functions in non-small cell lung cancer].

OBJECTIVE: To construct a lentiviral-vector-mediated CyPA small interference RNA (siRNA) and study its function in non-small cell lung cancer. METHODS: First, four target sequences were selected according to CyPA mRNA sequence, the complementary DNA contained both sense and antisense oligonucleotides were designed, synthesized and cloned into the pGCL-GFP vector, which contained U6 promoter and green fluorescent protein (GFP). The resulting lentiviral vector containing CyPA shRNA was named Lv-shCyPA, and it was confirmed by PCR and sequencing. Next, it was cotransfected by Lipofectamine 2000 along with pHelper1.0 and pHelper 2.0 into 293T cells to package lentivirus particles. At the same time, the packed virus infected non-small cell lung cancer cell (A549), the level of CyPA protein at 5 d after infection was detected by Western Blot to screen the target of CyPA. A549 were infected with Lv-shCyPA and grown as xenografts in severe combined immunodeficient mice. Cell cycle and apoptosis were measured by FCM. RESULTS: It was confirmed by PCR and DNA sequencing that lentiviral-vector-mediated CyPA siRNA (Lv-shCyPA) producing CyPA shRNA was constructed successfully. The titer of concentrated virus were 1 x 10(7) TU/ml. Flow cytometric analysis demonstrated G2-M phase (11.40% +/- 0.68%) was decreased relatively in A549/LvshCyPA compared with control groups (14.52% +/- 1.19%) (P<0.05). The apoptosis rate of A549/Lv-shCyPA (5.01% +/- 0.5%) was higher than control groups (0.35% +/- 0.17%) (P<0.05). Visible tumors were only detectable at 6th day after inoculated by A549/Lv-shCyPA. The xenograft tumors of A549/Lv-shCyPA remarkably delayed tumor growth and remained at a similarly small average size at 38th days after inoculation compared with the control group (P < 0.05). CONCLUSION: Lentiviral-vector-mediated siRNA technique effectively inhibits the expression of CyPA, induces the NSCLC cell apoptosis, inhibits the tumor growth. Elucidation of the precise role of CypA in these pathways may lead to new targeted therapies for non-small cell lung cancer.

Suicides and medically serious attempters are of the same population in Chinese rural young adults.

BACKGROUND: Suicide rates in China are among the highest in the world, although there has been a decreasing trend in the past few years. One practical approach to study the characteristics and risk factors of suicide is to interview the suicide attempters. It was to compare completed suicides with serious attempters that may shed lights on suicide prevention strategies. METHOD: This is a combination of two case control studies for suicide completers and suicide attempters respectively. After a sample of suicides (n=392) and community living controls (n=416) were obtained and studied in rural China, we collected in the same rural areas data of suicide attempt and studied 507 medically serious attempters and 503 community counterparts. RESULTS: Characteristics and previously observed risk factors were compared between the suicides and the attempters, and we found that the demographic characteristics and risk factors for the suicides were also for the medically serious attempters but at some lesser degrees for the attempters than for the suicides. It was especially true of suicide intent, deficient coping, negative life events, and impulsivity. While most of the demographic characteristics were not significantly different between the suicides and the attempters, most of the clinical variables could distinguish the two groups. CONCLUSIONS: The suicide victims and the serious attempters could be of the same group of people who were at the edge of fatal self-injury, and the same clinical risk factors but of different degrees have divided them into the life and death groups.

Risk factors for rural young suicide in China: a case-control study.

BACKGROUND: Suicide is the fifth most important cause of death in China and the leading cause of death among young adults aged 15-34 years. The suicide rate in rural China is three times higher than the urban suicide rate, and the rate in women is higher than in men. METHODS: Sixteen counties from three provinces were selected as sampling sites in which 392 suicide cases and 416 community living controls were obtained. For each suicide case and control there were two informants who provided the target person's information. A structured questionnaire including demographics, social and familial environments, and personal characteristics was administered to the informants. RESULTS: Mental disorders and high hopelessness were found to be strongly related to suicide among Chinese rural young adults. Other suicide risk factors among this population were negative life events, never married but dating, suicide history in family, lack of positive coping skills, lack of social support, dysfunctional impulsivity, and not being a Communist Party/League member. CONCLUSIONS: The prevalence of mental disorders, although the strongest risk factor among rural young adult suicides in this study, was markedly lower than that in Western countries. Some of the risk factors found in the comprehensive analyses are specific to Chinese culture. "Being a Communist Party/League member" as a protective factor for suicide among Chinese rural youths requires further study and appropriate interpretation.

Characterization of the spike protein of human coronavirus NL63 in receptor binding and pseudotype virus entry.

The spike (S) protein of human coronavirus NL63 (HCoV-NL63) mediates both cell attachment by binding to its receptor hACE2 and membrane fusion during virus entry. We have previously identified the receptor-binding domain (RBD) and residues important for RBD-hACE2 association. Here, we further characterized the S protein by investigating the roles of the cytoplasmic tail and 19 residues located in the RBD in protein accumulation, receptor binding, and pseudotype virus entry. For these purposes, we first identified an entry-efficient S gene template from a pool of gene variants and used it as a backbone to generate a series of cytoplasmic tail deletion and single residue substitution mutants. Our results showed that: (i) deletion of 18aa from the C-terminus enhanced the S protein accumulation and virus entry, which might be due to the deletion of intracellular retention signals; (ii) further deletion to residue 29 also enhanced the amount of S protein on the cell surface and in virion, but reduced virus entry by 25%, suggesting that residues 19-29 contributes to membrane fusion; (iii) a 29aa-deletion mutant had a defect in anchoring on the plasma membrane, which led to a dramatic decrease of S protein in virion and virus entry; (iv) a total of 15 residues (Y498, V499, V531, G534, G537, D538, S540, G575, S576, E582, W585, Y590, T591, V593 and G594) within RBD were important for receptor binding and virus entry. They probably form three receptor binding motifs, and the third motif is conserved between NL63 and SARS-CoV.

Rhesus angiotensin converting enzyme 2 supports entry of severe acute respiratory syndrome coronavirus in Chinese macaques.

Angiotensin converting enzyme 2 (ACE2) is the receptor that severe acute respiratory syndrome coronavirus (SARS-CoV) utilizes for target cell entry and, therefore, plays an important role in SARS pathogenesis. Since Chinese rhesus (rh) macaques do not usually develop SARS after SARS-CoV infection, it has been suggested that rh-ACE2 probably does not support viral entry efficiently. To determine the role of rh-ACE2 in early lung pathogenesis in vivo, we studied eleven Chinese rhesus monkeys experimentally infected with a pathogenic SARS-CoV(PUMC01) strain. Rh-ACE2 genes were amplified from all animals by reverse transcription polymerase chain reaction, and their function was studied in vitro using a pseudovirus entry assay. Many natural non-synonymous (NS) changes were found in rh-ACE2 genes. Compared to human (hu) ACE2, thirty-eight consensus NS changes were found in rh-ACE2. Since these changes do not interact with the receptor binding domain of SARS-CoV, rh-ACE2 in general is as effective as human homolog in supporting viral entry. Rh-ACE2, however, is more polymorphic than hu-ACE2. Additional sporadic NS substitutions in clone Rh11-7 reduced the level of rh-ACE2 protein expression and did not support viral entry effectively. Further mutagenesis analysis showed that a natural mutation Y217N dramatically alters ACE2 expression and entry efficiency. Moreover, introduction of the Y217N mutation into hu-ACE2 caused the down-regulation of expression and reduced viral entry efficiency. These results indicate that the Y217N mutation plays a role in modulating SARS-CoV infection. Our results provide insights for understanding the role of rh-ACE2 in SARS lung pathogenesis in a non-human primate model.

Detection of viral agents in fecal specimens of monkeys with diarrhea.

BACKGROUND: Diarrheal disease is a major cause of morbidity and mortality in humans and animals, including non human primates. While the diagnostics for gastrointestinal bacterial and parasitic pathogens and their etiological role in disease are well established, little is known about the epidemiology, prevalence and role of viral agents in diarrheal illness among monkeys. METHODS: We collected fecal specimens from monkeys with diarrhea that were housed in two primate colonies, the Institute of Laboratory Animal Sciences, Beijing, China and the Yerkes National Primate Research Center, Georgia, USA. We screened these fecal specimens for rotaviruses and enteric adenoviruses 40/41 by using commercial EIA kits (Rotaclone and Adenoclone), enteroviruses by RT-PCR and Southern blot hybridization, and picobirnaviruses by polyacrylamide gel electrophoresis and silver staining. Some of the specimens were examined by EM for coronaviruses and noroviruses. RESULTS: Of the 92 specimens from China, we found 63 (68%) positive for viruses, including enteroviruses (52%), enteric adenoviruses (21%), rotaviruses (20%), and picobirnaviruses (2%). Coronaviruses were detected in some specimens. Mixed infection of two or more viral agents was seen in 23 (25%) specimens. In the US collection, we detected enteroviruses and enteric adenoviruses in 76% (45/59) and 14% (7/50) of the specimens, respectively. Electron microscopy showed norovirus-like particles in some specimens from both colonies. CONCLUSIONS: Our findings indicate endemic infections with enteric viruses in monkeys of both colonies. The availability of new simian rotaviruses, enteric adenoviruses, enteroviruses, and coronaviruses and the discovery of noroviruses and picobirnaviruses may allow us to develop better diagnostics for these agents and determine which of these agents are clearly associated with gastroenteritis in monkeys.

[Preventive and therapeutic effects of recombinant IFN-alpha2b nasal spray on SARS-CoV infection in Macaca mulata].

OBJECTIVE: To study the preventive and therapeutic effects of recombinant IFN-alpha2b for nasal spray on SARS-CoV infection in Macaca mulata (rhesus monkey). METHODS: Ten rhesus monkeys were divided into two groups, 5 in interferon group, and 5 in control group. Before and after SARS-CoV attack, the virus was detected in samples such as pharyngeal swab in all the two groups by Real-time PCR (RT-PCR) and virus isolation was performed. RESULTS: After virus attack, the level of SARS-CoV-specific IgG and neutralizing antibody were induced by SARS-CoV in the interferon group was weaker than in control group. Hematology items showed no apparent changes after virus attack in treated group. Through pathological examination, the morphology of the lung tissues of two Macaques in the treated group was normal, while the other three displayed the interstitial pneumonia with the thickened septum and infiltration with mononuclear cells. Among which, one monkey showed part of thickened septum fused with each other. These lesions in the interferon treated animals were similar to those seen in the animals in control group, but with smaller scope of pathological changes. No significant abnormity was detected in other organs. CONCLUSION: Recombinant IFN-alpha2b could effectively interdict or weaken SARS-CoV injury in monkeys.

Recombinant modified vaccinia virus Ankara expressing the spike glycoprotein of severe acute respiratory syndrome coronavirus induces protective neutralizing antibodies primarily targeting the receptor binding region.

Immunization with a killed or inactivated viral vaccine provides significant protection in animals against challenge with certain corresponding pathogenic coronaviruses (CoVs). However, the promise of this approach in humans is hampered by serious concerns over the risk of leaking live severe acute respiratory syndrome (SARS) viruses. In this study, we generated a SARS vaccine candidate by using the live-attenuated modified vaccinia virus Ankara (MVA) as a vector. The full-length SARS-CoV envelope Spike (S) glycoprotein gene was introduced into the deletion III region of the MVA genome. The newly generated recombinant MVA, ADS-MVA, is replication incompetent in mammalian cells and highly immunogenic in terms of inducing potent neutralizing antibodies in mice, rabbits, and monkeys. After two intramuscular vaccinations with ADS-MVA alone, the 50% inhibitory concentration in serum was achieved with reciprocal sera dilutions of more than 1,000- to 10,000-fold in these animals. Using fragmented S genes as immunogens, we also mapped a neutralizing epitope in the region of N-terminal 400 to 600 amino acids of the S glycoprotein (S400-600), which overlaps with the angiotensin-converting enzyme 2 (ACE2) receptor-binding region (RBR; S318-510). Moreover, using a recombinant soluble RBR-Fc protein, we were able to absorb and remove the majority of the neutralizing antibodies despite observing that the full S protein tends to induce a broader spectrum of neutralizing activities in comparison with fragmented S proteins. Our data suggest that a major mechanism for neutralizing SARS-CoV likely occurs through blocking the interaction between virus and the cellular receptor ACE2. In addition, ADS-MVA induced potent immune responses which very likely protected Chinese rhesus monkeys from pathogenic SARS-CoV challenge.

An animal model of SARS produced by infection of Macaca mulatta with SARS coronavirus.

A new SARS animal model was established by inoculating SARS coronavirus (SARS-CoV) into rhesus macaques (Macaca mulatta) through the nasal cavity. Pathological pulmonary changes were successively detected on days 5-60 after virus inoculation. All eight animals showed a transient fever 2-3 days after inoculation. Immunological, molecular biological, and pathological studies support the establishment of this SARS animal model. Firstly, SARS-CoV-specific IgGs were detected in the sera of macaques from 11 to 60 days after inoculation. Secondly, SARS-CoV RNA could be detected in pharyngeal swab samples using nested RT-PCR in all infected animals from 5 days after virus inoculation. Finally, histopathological changes of interstitial pneumonia were found in the lungs during the 60 days after viral inoculation: these changes were less marked at later time points, indicating that an active healing process together with resolution of an acute inflammatory response was taking place in these animals. This animal model should provide insight into the mechanisms of SARS-CoV-related pulmonary disease and greatly facilitate the development of vaccines and therapeutics against SARS.

[Potent neutralization antibody elicited in mice by SARS-associated coronavirus spike protein S1 domain].

OBJECTIVE: To study the antigenicity of SARS associated coronavirus (CoV) spike S1 (12-672Aa) domain. METHODS: BALB/c mice were immunized with a plasmid bearing codon-optimized SARS-CoV (Tor2 strain) S1 domain and then boosted with purified S1 protein; the SARS-CoV specific IgG antibody was tested by ELISA and neutralization antibody was determined by in vitro microneutralization assay. RESULTS: S1 domain of SARS-CoV spike, which has been demonstrated harboring the receptor binding domain, successfully elicited SARS-CoV specific IgG antibody in mouse after combined immunization with DNA and purified S1 protein; the antibody elicited solely by S1 could potently neutralize SARS-CoV (HKU-39849) in vitro, 50% of 1 000 TCID50 SARS-CoV challenged cells were protected from viral infection by a 1:1499.68 dilution of mice sera immunized with S1 protein, but negative control sera showed no protection. CONCLUSION: S1 domain of SARS-CoV spike protein, which is responsible for receptor binding, can efficiently and sufficiently induce highly potent neutralizing antibody in mice. This result suggested that S1 domain could be an effective subunit vaccines against SARS-CoV.